The use of cross-species genome-wide arrays to discover SNP markers for conservation genetics: a case study from Arabian
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TECHNICAL NOTE
The use of cross-species genome-wide arrays to discover SNP markers for conservation genetics: a case study from Arabian and scimitar-horned oryx Rob Ogden • Jan Baird • Helen Senn Ross McEwing
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Received: 4 June 2010 / Accepted: 12 November 2011 / Published online: 24 November 2011 Ó Springer Science+Business Media B.V. 2011
Abstract The potential use of single nucleotide polymorphism markers (SNPs) in conservation genetics is widely recognized; however, methods for discovering large numbers of SNPs typically rely on relatively expensive, genome-wide, species-specific research projects which limits their development in many taxa. Here we describe the use of high-density SNP genotyping arrays designed for cattle to discover SNPs in two antelope species. From a total of 54,001 SNP markers on the array, the analysis yielded 148 polymorphic markers in the scimitar-horned oryx and 149 in the Arabian oryx. The results represent a first step toward developing SNP marker panels for ongoing projects on each species. As high density genotyping arrays become available for an increasing number of model species, this approach has the potential to generate SNP markers, rapidly and affordably, in a broad range of species for conservation genetic research. Keywords SNP discovery Non-model species Bovine SNP50 Conservation genomics
Electronic supplementary material The online version of this article (doi:10.1007/s12686-011-9577-2) contains supplementary material, which is available to authorized users. R. Ogden (&) H. Senn R. McEwing Wildgenes Laboratory, Royal Zoological Society of Scotland, Edinburgh EH12 6TS, UK e-mail: [email protected] J. Baird Gen-Probe Life Sciences, Appleton Place, Livingston EH54 7EZ, UK
Introduction The potential application of SNP markers to conservation genetics has long been recognized (Morin et al. 2004; Luikart et al. 2003) and is central to the emerging field of conservation genomics (Avise 2010; Ouborg et al. 2010); however, the actual discovery of SNPs in non-model species has remained problematic. The development of highthroughput sequencing technologies has raised the possibility of using genome-wide approaches to discover SNPs; these have been successfully applied to model species and are now being examined in non-model organisms of conservation interest however, the large number of species and per species cost of high-throughput sequencing currently limits widespread use in the conservation genetic community. The Illumina bovine SNP50 array enables the simultaneous genotyping of 54,001 mapped SNP markers. It has been widely employed to genotype bovids to support cattle improvement programmes (Snelling et al. 2010) and examine diversity within and among cattle breeds (Wilkinson et al. 2011). Decker et al. (2009) also demonstrated its utility in phylogenetic reconstruction of ruminants, highlighting the potential for cross-species amplification of SNP markers. Here we take this concept further by examining the potential for identifying SNP markers for population ge
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